Yeah it is kinda homework. it is a Drosophila melanogaster genome.
• 0 views
•
link
written
by
mohammadborooshaki •
Introns identification in genome reference file
Hi everybody
I have a reduced genome fasta files which has only one chromosome(not the whole genome). this is a refrence genome(not transcriptome). how can I identify the introns and exons from a fasta file? what I have to do for my project is to remove the introns but I do not know how to distinguish them. Is there a way to find the introns from a fasta file? Thanks for any help
• 1,232 views
•
link
updated
by
ATpoint
•
written
by
mohammadborooshaki •
•
written
by
mohammadborooshaki •
1 answer
What genome are you working with ? Is this home work ? If its home work, try to get the GTF file for the genome and then fetch transcriptome from gffread which excludes introns. If you are skilled at programming, you could also write a script to extract parts of fasta sequence that overlap exon coordinates from GTF.
If you dont have a reference GTF, you may need to depend on some gene prediction tools.
• 0 views
•
link
written
by
GouthamAtla
Log in to answer this question.
More posts like this
-
Filter intergenic regions in a .bed file
written by paulklein05 •
-
extract exons/introns from multiple fasta files with gene sequences
written by ramiroricardo •
-
Detecting GC Bias in Transcriptomes (RNA-seq)
written by Jon17 •
-
Finding exons and introns sequences
written by elisheva
-
Generation of Consenses Fasta from SAM/BAM
written by mail2steff
-
How to extract fasta from 1000 genomes?
written by martingarridorc •
-
Biological difference for selecting alignment reference to DNA vs cDNA
written by bharata1803
-
Problem Viewing Alignments in IGV When Loading Custom FASTA file
written by moldach
-
identifying genes in unknown sequence
written by anabas_10 •
-
Identification Of Promoters From Gene Sequences And A Vertebrate Genome Assembly
written by David M
